[gmx-users] radial distribution function

[Justin Lemkul]

On 6/30/18 12:15 PM, kordzadeh at aut.ac.ir wrote:
> ​Hi all
> when we calculate RDF, we have g(r) versus radius, please tell me, what is this radius, is it the distance between center of mass of two component or is it the radius of a sphere that is consider for probability of finding molecules,

I suggest you read manual section 8.4.

> what is difference between -com and -xy?

They don't necessarily have anything to do with one another.

The -com option means to compute g(r) with respect to the center-of-mass 
of the selected group.

The -xy option uses only the distance along the x-y plane rather than 
the full (x,y,z) distance.

> if I want to calculate RDF from axis of CNT, should I use -xy option?

If the CNT axis is aligned directly along z, perhaps.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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